Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms

Local adaptation is facilitated by loci clustered in relatively few regions of the genome, termed genomic islands of divergence. The mechanisms that create and maintain these islands and how they contribute to adaptive divergence is an active research topic. Here, we use sockeye salmon as a model to investigate both the mechanisms responsible for creating islands of divergence and the patterns of differentiation at these islands. Previous research suggested that multiple islands contributed to adaptive radiation of sockeye salmon. However, the low-density genomic methods used by these studies made it difficult to fully elucidate the mechanisms responsible for islands and connect genotypes to adaptive variation. We used whole genome resequencing to genotype millions of loci to investigate patterns of genetic variation at islands and the mechanisms that potentially created them. We discovered 64 islands, including 16 clustered in four genomic regions shared between two isolated population...,
Sampling design 
We resequenced genomes of sockeye salmon from seven populations in Southwest Alaska, USA (these samples are a subset of those analyzed in Larson et al., 2019). Fin-clips from 27 individuals per population (189 individuals total) were obtained from three lake-type spawning populations in each of the Kvichak River and Wood River drainages as well as one putatively ancestral sea/river population in the Nushagak River drainage. Lake-type samples were further subdivided into the following groups based on spawning habitat: mainland beaches, island beaches, creeks, and rivers. Mainland and island beaches are similar except island beaches are found in the middle of lakes where they are highly affected by wind and wave action (Stewart et al., 2003). Creeks are narrow (< 5 m wide) and shallow (< 0.5 m deep on average) while rivers are wide (> 30 m wide), deep (> 0.5 m deep), and fast flowing (Quinn et al., 2001). All samples were collected from spawning adults by Ala..., , # Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms

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The following files include genotype files in variant call format (VCF) for all sockeye salmon genotyped for the associated publication by the same name published in Molecular Ecology in 2023.

## Description of the data and file structure

*VCF file descriptions*

**LG1-29\_output.recalibrated.filtered.vcf.gz** includes the raw genotype calls for all possible variants identified by GATK4. These data were subsequently re-calibrated using known SNP variants and filtered (see manuscript for filtering details) resulting in file **LG1-29\_output.recalibrated.filtered.1.no-indels.no-fail.biallele.miss.0.9.maf.0.05.ab.0.2.vcf.gz** which was used for downstream analysis. variant index files (.idx) are also included for both files.

To assess rangewide consistency in haplotypes, data were merged with existing sockeye salmon whole genome sequencing data from Christen...